Smith-Waterman peak alignment for comprehensive two-dimensional gas chromatography-mass spectrometry.
Smith-Waterman peak alignment for comprehensive two-dimensional gas chromatography-mass spectrometry.
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DOI：
10.1186/1471-2105-12-235
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发表时间：
2011-06-15
影响因子：
3
通讯作者：
Zhang X
中科院分区：
文献类型：
--
作者：
Kim S;Koo I;Fang A;Zhang X
综合二维气相色谱-质谱联用（GC × GC- ms）是一种强大的技术，在过去的二十年中得到了越来越多的关注。GC × GC- ms为复杂样品分析提供了更大的分离能力、化学选择性和灵敏度，并提供了更准确的化合物保留时间和质谱信息。尽管有这些优点，但由于实验的变化，二维气相色谱柱上解析峰的保留时间总是发生变化，这给代谢组学分析的数据处理带来了困难。因此，为了比较不同条件下获得的多种代谢谱，必须调整保留时间的变化。我们利用改进的Smith-Waterman局部对齐算法和质谱相似度，开发了针对同质（在相同实验条件下获得）和异质（在不同实验条件下获得）GC × GC- ms数据的新的峰对齐算法。与文献报道的算法相比，本文算法消除了地标峰检测和保留时间变换的使用。在此基础上，通过实现最优峰对的似然函数，构建了自动峰对软件包。本文提出的Smith-Waterman局部对准算法能够同时对准多个GC × GC- ms实验的同质和异构数据，而不需要改变保留时间和选择地标峰。基于关联似然函数，建立了基于sw的自动峰对算法的优化版本。本文提出的比对算法优于文献报道的比对方法，通过分析复方标准品和小鼠血浆代谢物提取物的混合实验数据。
Comprehensive two-dimensional gas chromatography coupled with mass spectrometry (GC × GC-MS) is a powerful technique which has gained increasing attention over the last two decades. The GC × GC-MS provides much increased separation capacity, chemical selectivity and sensitivity for complex sample analysis and brings more accurate information about compound retention times and mass spectra. Despite these advantages, the retention times of the resolved peaks on the two-dimensional gas chromatographic columns are always shifted due to experimental variations, introducing difficulty in the data processing for metabolomics analysis. Therefore, the retention time variation must be adjusted in order to compare multiple metabolic profiles obtained from different conditions. We developed novel peak alignment algorithms for both homogeneous (acquired under the identical experimental conditions) and heterogeneous (acquired under the different experimental conditions) GC × GC-MS data using modified Smith-Waterman local alignment algorithms along with mass spectral similarity. Compared with literature reported algorithms, the proposed algorithms eliminated the detection of landmark peaks and the usage of retention time transformation. Furthermore, an automated peak alignment software package was established by implementing a likelihood function for optimal peak alignment. The proposed Smith-Waterman local alignment-based algorithms are capable of aligning both the homogeneous and heterogeneous data of multiple GC × GC-MS experiments without the transformation of retention times and the selection of landmark peaks. An optimal version of the SW-based algorithms was also established based on the associated likelihood function for the automatic peak alignment. The proposed alignment algorithms outperform the literature reported alignment method by analyzing the experiment data of a mixture of compound standards and a metabolite extract of mouse plasma with spiked-in compound standards.
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影响因子：
4.1
作者：
Oh, Cheolhwan;Huang, Xiaodong;Zhang, Xiang
通讯作者：
Zhang, Xiang
影响因子：
7.4
作者：
Pierce, KM;Wood, LF;Synovec, RE
通讯作者：
Synovec, RE
影响因子：
4.1
作者：
van Mispelaar, VG;Tas, AC;van Asten, AC
通讯作者：
van Asten, AC
DOI：
10.1007/b137845
发表时间：
2005-01-01
期刊：
STATISTICAL METHODS IN BIOINFORMATICS: AN INTRODUCTION
影响因子：
--
作者：
Ewens, W.;Grant, G.
通讯作者：
Grant, G.
影响因子：
2
作者：
Liu J;Bell AW;Bergeron JJ;Yanofsky CM;Carrillo B;Beaudrie CE;Kearney RE
通讯作者：
Kearney RE